In their paper “Sixteen Days” Barry Smith and Berit Brogaard try to answer the question: when does a human being begin to exist? In this paper we will address some methodological issues connected with this exercise in ontology. We shall begin by sketching the argument of “Sixteen Days”. We shall then attempt to characterize what is special about the ontological realism of “Sixteen Days” as contrasted to the linguistic constructivism which represents the more dominant current in contemporary analytic philosophy. (...) This will allow us to infer guidelines for assessing the quality of ontological theories of various types. We shall argue that ontological parsimony, groundedness, faithfulness to ordinary language, consistency with science, coherence, and fruitfulness are at least part of the adequacy criteria for such theories. These criteria will then be applied to the theory presented in “Sixteen Days”, and they will lead us to some revisions of this theory as well as to some reflections on its ethical implications. (shrink)

We advance a model of human probability judgment and apply it to the design of an extrapolation algorithm. Such an algorithm examines a person's judgment about the likelihood of various statements and is then able to predict the same person's judgments about new statements. The algorithm is tested against judgments produced by thirty undergraduates asked to assign probabilities to statements about mammals.

Establishing reasonable, prior distributions remains a significant obstacle for the construction of probabilistic expert systems. Human assessment of chance is often relied upon for this purpose, but this has the drawback of being inconsistent with axioms of probability. This article advances a method for extracting a coherent distribution of probability from human judgment. The method is based on a psychological model of probabilistic reasoning, followed by a correction phase using linear programming.

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...) them. However, such ‘minimum information’ MI checklists are usually developed independently by groups working within representatives of particular biologically- or technologically-delineated domains. Consequently, an overview of the full range of checklists can be difficult to establish without intensive searching, and even tracking thetheir individual evolution of single checklists may be a non-trivial exercise. Checklists are also inevitably partially redundant when measured one against another, and where they overlap is far from straightforward. Furthermore, conflicts in scope and arbitrary decisions on wording and sub-structuring make integration difficult. This presents inhibit their use in combination. Overall, these issues present significant difficulties for the users of checklists, especially those in areas such as systems biology, who routinely combine information from multiple biological domains and technology platforms. To address all of the above, we present MIBBI (Minimum Information for Biological and Biomedical Investigations); a web-based communal resource for such checklists, designed to act as a ‘one-stop shop’ for those exploring the range of extant checklist projects, and to foster collaborative, integrative development and ultimately promote gradual integration of checklists. (shrink)

This paper will attempt to assess the primary differences between what I take to be the two primary philosophical "traditions" in contemporary French philosophy, using Derrida (transcendence) and Deleuze (immanence) as exemplary representatives. The body of the paper will examine the use of these terms in three different areas of philosophy on which Derrida and Deleuze have both written: subjectivity, ontology, and epistemology. (1) In the field of subjectivity, the notion of the subject has been critiqued in two manners, either (...) by appealing either to the transcendence of the other (Levinas, Derrida) or to the immanent jlux of experience itself, in relation to which the Ego itself is trancendent (Deleuze, Foucault, Sartre, James). (2) In the field of ontology, a purely "immanent" ontology would be an ontology in which there is neither a "beyond" or an "otherwise" Being, nor "interruptions" in Being, both of which would require an appeal to a formal element of transcendence (Deleuze). Such a "transcendent" and aporetic structure, which can never appear or be present as such within Being, is what lies at the basis of the project of deconstruction, with its attendant aporias (Derrida). (3) This distinction, finally, finds parallels in Kant's epistemology, for whom the possible experience is conditioned by purely immanent criteria (Deleuze), whereas what goes beyond the limits of possible experience is transcendent (Derrida). Drawing on these three thread of analysis, the paper concludes with an assessment of what is at stake in the ethical differences between the two traditions. The question of "transcendence" is "What mast I do?", which is the question of morality (a duty or obligation that is beyond being, an "ought" beyond the "is"). The question of "immanence" is "What can I do?" (my power or capacity as an existing individual within being). For Levinas and Derrida, ethics precedes ontology because it is derived from an element of transcendence (the Other); for Deleuze, ethics is ontology because it is derived from the immanent relation of beings to Being at the level of their existence (Spinoza). (shrink)

This paper examines the intersecting of the themes of temporality and truth in Deleuze's philosophy. For the ancients, truth was something eternal: what was true was true in all times and in all places. Temporality (coming to be and passing away) was the realm of the mutable, not the eternal. In the seventeenth century, change began to be seen in a positive light (progress, evolution, and so on), but this change was seen to be possible only because of the immutable (...) laws of nature that govern change. It was not until philosophers such as Bergson, James, Whitehead – and then Deleuze – that time began to be taken seriously on its own account. On the one hand, in Deleuze, time, freed from its subordination to movement, now becomes autonomous: it is the pure form of change (continuous variation) that lies at the basis of Deleuze's metaphysics in Difference and Repetition (and is explored more thematically in The Time-Image). As a result, on the other hand, the false, freed from its subordination to the form of the true, assumes a power of its own (the power of the false), which in turn implies a new ‘analytic of the concept’ that Deleuze develops in What Is Philosophy? (shrink)

Difference and Repetition might be said to have brought about a Deleuzian Revolution in philosophy comparable to Kant’s Copernican Revolution. Kant had denounced the three great terminal points of traditional metaphysics – self, world and God – as transcendent illusions, and Deleuze pushes Kant’s revolution to its limit by positing a transcendental field that excludes the coherence of the self, world and God in favour of an immanent and differential plane of impersonal individuations and pre-individual singularities. In the process, he (...) introduces numerous conceptual innovations into philosophy: the becoming of concepts; a transformation of the form of the question; an insistence that philosophy must start in the middle; an attempt to think in terms of multiplicities; the development of a new logic and a new metaphysics based on a concept of difference; a new conception of space as intensive rather than extensive; a conception of time as a pure and empty form; and an understanding of philosophy as a system in heterogenesis – that is, a system that entails a perpetual genesis of the heterogeneous, an incessant production of the new. -/- Keywords: concepts, becoming, multiplicity, singularity, the middle [au milieu], difference, intensity, time, system, the new. (shrink)

Cross-situational word learning, like any statistical learning problem, involves tracking the regularities in the environment. However, the information that learners pick up from these regularities is dependent on their learning mechanism. This article investigates the role of one type of mechanism in statistical word learning: competition. Competitive mechanisms would allow learners to find the signal in noisy input and would help to explain the speed with which learners succeed in statistical learning tasks. Because cross-situational word learning provides information at multiple (...) scales—both within and across trials/situations—learners could implement competition at either or both of these scales. A series of four experiments demonstrate that cross-situational learning involves competition at both levels of scale, and that these mechanisms interact to support rapid learning. The impact of both of these mechanisms is considered from the perspective of a process-level understanding of cross-situational learning. (shrink)

Machine generated contents note: Introduction Henry Somers-Hall; 1. Deleuze and the history of philosophy Daniel W. Smith; 2. Difference and repetition James Williams; 3. The Deleuzian reversal of Platonism Miguel Beistegui; 4. Deleuze and Kant Beth Lord; 5. Phenomenology and metaphysics, and chaos: on the fragility of the event in Deleuze Leonard Lawlor; 6. Deleuze and structuralism François Dosse; 7. Deleuze and Guattari: Guattareuze and Co. Gary Genosko; 8. Nomadic ethics Rosi Braidotti; 9. Deleuze's political philosophy Paul Patton; 10. (...) Deleuze, mathematics, and realist ontology Manuel Delanda; 11. Deleuze and life John Protevi; 12. Gilles Deleuze's aesthetics of sensation Dorothea Olkowski; 13. Deleuze and literature Ronald Bogue; 14. Deleuze and psychoanalysis Eugene Holland; 15. Deleuze's philosophical heritage: unity, difference, and onto-theology Henry Somers-Hall. (shrink)

Ontology is a burgeoning field, involving researchers from the computer science, philosophy, data and software engineering, logic, linguistics, and terminology domains. Many ontology-related terms with precise meanings in one of these domains have different meanings in others. Our purpose here is to initiate a path towards disambiguation of such terms. We draw primarily on the literature of biomedical informatics, not least because the problems caused by unclear or ambiguous use of terms have been there most thoroughly addressed. We advance a (...) proposal resting on a distinction of three levels too often run together in biomedical ontology research: 1. the level of reality; 2. the level of cognitive representations of this reality; 3. the level of textual and graphical artifacts. We propose a reference terminology for ontology research and development that is designed to serve as common hub into which the several competing disciplinary terminologies can be mapped. We then justify our terminological choices through a critical treatment of the ‘concept orientation’ in biomedical terminology research. (shrink)

Integrating concepts of maintenance and of origins is essential to explaining biological diversity. The unified theory of evolution attempts to find a common theme linking production rules inherent in biological systems, explaining the origin of biological order as a manifestation of the flow of energy and the flow of information on various spatial and temporal scales, with the recognition that natural selection is an evolutionarily relevant process. Biological systems persist in space and time by transfor ming energy from one state (...) to another in a manner that generates structures which allows the system to continue to persist. Two classes of energetic transformations allow this; heat-generating transformations, resulting in a net loss of energy from the system, and conservative transformations, changing unusable energy into states that can be stored and used subsequently. All conservative transformations in biological systems are coupled with heat-generating transformations; hence, inherent biological production, or genealogical proesses, is positively entropic. There is a self-organizing phenomenology common to genealogical phenomena, which imparts an arrow of time to biological systems. Natural selection, which by itself is time-reversible, contributes to the organization of the self-organized genealogical trajectories. The interplay of genealogical (diversity-promoting) and selective (diversity-limiting) processes produces biological order to which the primary contribution is genealogical history. Dynamic changes occuring on times scales shorter than speciation rates are microevolutionary; those occuring on time scales longer than speciation rates are macroevolutionary. Macroevolutionary processes are neither redicible to, nor autonomous from, microevolutionary processes. (shrink)

We have synthesized a 582,970-base pair Mycoplasma genitalium genome. This synthetic genome, named M. genitalium JCVI-1.0, contains all the genes of wild-type M. genitalium G37 except MG408, which was disrupted by an antibiotic marker to block pathogenicity and to allow for selection. To identify the genome as synthetic, we inserted "watermarks" at intergenic sites known to tolerate transposon insertions. Overlapping "cassettes" of 5 to 7 kilobases (kb), assembled from chemically synthesized oligonucleotides, were joined by in vitro recombination to produce intermediate (...) assemblies of approximately 24 kb, 72 kb ("1/8 genome"), and 144 kb ("1/4 genome"), which were all cloned as bacterial artificial chromosomes in Escherichia coli. Most of these intermediate clones were sequenced, and clones of all four 1/4 genomes with the correct sequence were identified. The complete synthetic genome was assembled by transformation-associated recombination cloning in the yeast Saccharomyces cerevisiae, then isolated and sequenced. A clone with the correct sequence was identified. The methods described here will be generally useful for constructing large DNA molecules from chemically synthesized pieces and also from combinations of natural and synthetic DNA segments. 10.1126/science.1151721. (shrink)

The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create (...) new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Philosophy and Rhetoric 36.2 (2003) 172-176 [Access article in PDF] The Rhetorical Imagination of Kenneth Burke. Studies in Rhetoric/Communication. Ross Wolin. Series ed. Thomas W. Benson. Columbia, SC: University of South Carolina Press, 2001. Pp. xviii + 256. $34.95, cloth. Ross Wolin's The Rhetorical Imagination of Kenneth Burke offers its readers an interesting mix of intellectual history and conceptual explication, along with an element of biography, which Wolin performs (...) in an effort to trace the movements of Burke's thought as it developed over time within particular socio-political circumstances. The book is divided into three parts, each corresponding to Wolin's three-part division of Burke's intellectual [End Page 172] career. Part I, "Towards a Better Life through Art, Criticism and Politics," begins with a chapter on Burke's formation as a critic in the bohemian, avant-garde culture of post-World War I Greenwich Village. Wolin offers an account of how the dynamics of this social milieu prompted Burke to incorporate politics into his already established aesthetic interests, and of this fusion's manifestation in left-leaning periodicals of the time. While some might be tempted to see this first chapter as having limited value in comparison to Jack Selzer's richly detailed Kenneth Burke in Greenwich Village : Conversing with the Moderns, 1915-1931, it should be noted that Wolin does a fine job of helping his readers—in chapter one and those which follow—to understand explicitly how specific contexts shaped Burke's ideas and his rhetoric (something that Selzer's book does not do). Wolin is particularly adept at showing how, for Burke, there is an inextricable link between aesthetics, rhetoric, politics, and social life in general. This aesthetic-rhetorical connection to politics and life, argues Wolin, is key to understanding all of Burke's work. According to Wolin, equally important is how this connection informed the essays that comprised Burke's Counter-Statement, which Wolin sees as the seed from which all of Burke's theoretical and critical writings grew. For Wolin, to understand Burke one must understand Counter-Statement, and understand it within the historical circumstances that prompted and shaped its concepts and their rhetorical presentation.Chapter two is thus devoted to a discussion of the significance of Counter-Statement within Burke's oeuvre. It is in Counter-Statement, Wolin contends, that one can discern not only the fundaments of Burke's later work but also the "Critics Credo" that organized Burke's rhetorical efforts from Permanence and Change to The Rhetoric of Religion. Wolin's attempt to demonstrate the operation of this credo in all of Burke's books as an organizing principle pushes the limits of credulity at times, but readers should not let this obscure the insight Wolin offers us into Burke's responses to and interventions in early twentieth-century intellectual culture. Chapters three, four, and five comprise Part II of Wolin's book, "The Tactics of Conflict and Cooperation," which discusses in succession the three books that followed Counter-Statement chronologically: Permanence and Change, Attitudes Towards History, and The Philosophy of Literary Form. In these chapters, Wolin makes numerous interesting and novel points about Burke's thought. In the chapter on Permanence and Change, for example, Wolin highlights the conception of ethics implicit in that work, one that has its roots in poetics (particularly tragedy) and which refuses "to supplant traditional [End Page 173] ethics with another system [that is] equally fixed" (77). Although he does not state this, implicit in Wolin's reading is the suggestion that within Burke's work lies an alternative to the neo-Aristotelian virtue ethics and Habermasian universal pragmatics so many rhetorical scholars seem to embrace when theorizing a rhetorical ethics. (A "dramatistic" ethics of discourse and public life is, I think, an untapped potential of Burke's work.) Part III, "The Tactics of Motivation," offers similarly insightful and contextualized readings of A Grammar of Motives, A Rhetoric of Motives, The Rhetoric of Religion, and Language as Symbolic Action. Particularly interesting is Wolin's discussion in chapter seven of the importance of style... (shrink)

We live in an era where our health is linked to that of others across the globe, and nothing brings this home better than the specter of a pandemic. This paper explores the findings of town hall meetings associated with the Canadian Program of Research on Ethics in a Pandemic , in which focus groups met to discuss issues related to the global governance of an influenza pandemic. Two competing discourses were found to be at work: the first was based (...) upon an economic rationality and the second upon a humanitarian rationality. The implications for public support and the long-term sustainability of new global norms, networks, and regulations in global public health are discussed. (shrink)

Gilles Deleuze was one of the most influential philosophers of the twentieth-century, and Smith is widely recognized to be one of his most penetrating interpreters, as well as an important philosophical voice in his own right. Combining his most important pieces over the last fifteen years along with two new essays, this book is Smith 's definitive treatise on Deleuze. The essays are divided into four sections, which cover Deleuze's use of the history of philosophy, an overview of (...) his philosophical system, an analysis of several Deleuzian concepts, as well as an assessment of his position within contemporary philosophy. (shrink)

A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these ontologies, while requiring considerable effort, is extremely desirable. However, heterogeneities in format and style pose serious obstacles to such integration. In particular, inconsistencies in naming conventions can impair the readability and navigability of ontology class hierarchies, and hinder their alignment and integration. While other sources of diversity are tremendously complex and challenging, agreeing (...) a set of common naming conventions is an achievable goal, particularly if those conventions are based on lessons drawn from pooled practical experience and surveys of community opinion. We summarize a review of existing naming conventions and highlight certain disadvantages with respect to general applicability in the biological domain. We also present the results of a survey carried out to establish which naming conventions are currently employed by OBO Foundry ontologies and to determine what their special requirements regarding the naming of entities might be. Lastly, we propose an initial set of typographic, syntactic and semantic conventions for labelling classes in OBO Foundry ontologies. Adherence to common naming conventions is more than just a matter of aesthetics. Such conventions provide guidance to ontology creators, help developers avoid flaws and inaccuracies when editing, and especially when interlinking, ontologies. Common naming conventions will also assist consumers of ontologies to more readily understand what meanings were intended by the authors of ontologies used in annotating bodies of data. (shrink)

Background: Studies have found that children with Autism Spectrum Disorder (ASD) are more likely to make errors in appropriately producing referring expressions (‘the dog’ vs. ‘the black dog’) than are controls but comprehend them with equal facility. We tested whether this anomaly arises because comprehension studies have focused on manipulating perspective-taking at a ‘generic speaker’ level. Method: We compared 24 autistic eight- to eleven-year-olds with 24 well-matched neuro-typical controls. Children interpreted requests (e.g. ‘Can I have that ball?’) in contexts which (...) would be ambiguous (i.e. because the child can see two balls) if perspective-taking were not utilized. In the interlocutor-specific perspective-taking condition, the target was the particular object which was new for the speaker. Children needed to take into account what the speaker had played with before and the fact that they were now expressing excitement about something new. In two control ‘speaker-generic’ conditions we tested children’s ability to take the visual perspective of the speaker (where any speaker who stood behind a particular barrier would have the same perspective). Results: The autistic group were significantly less likely to select the target and significantly more likely to request clarification in the ‘interlocutor-specific’ condition. Performance in the ‘interlocutor-generic’ (visual) perspective taking conditions did not differ between groups. Conclusion: Autistic children, even those who are not intellectually-impaired, tend to have more difficulty than neuro-typical peers in comprehending referring expressions when this requires understanding that people comment on what is new for them. (shrink)

Until recently, the history of environmentalism was primarily a history of attention to place. In the United States, environmentalists have gotten rather good at protecting and managing particular places such as mountains, forests, and watersheds and specific resources such as trees, soil, wildlife, air, and water. Environmentalism has become an enormously popular social movement, with, by some measures, more than 80 percent of Americans considering themselves environmentalists. Thousands of organizations, ranging from local volunteer groups to national nonprofits, address issues as (...) diverse as open space, air and water pollution, biological diversity, environmental justice, and environmental effects on human health. The successes of this movement have been striking. Our National Parks, National Forests, and wilderness areas are touted as models for the world and are well complemented by state, municipal, and private protected areas. The Endangered Species Act successfully resolves many conflicts between rare creatures and development. Rivers have been cleaned up, and once-spurned urban waterfronts now draw real estate and tourism development. Americans drink cleaner water and breathe cleaner air than much of the rest of the world, and attempts to weaken regulatory frameworks are consistently met with public disapproval. (shrink)

The volumes are self contained and can be used individually in upper-level undergraduate and graduate courses ranging from introductory psychology, linguistics, ...

The development of culture-independent strategies to study microbial diversity and function has led to a revolution in microbial ecology, enabling us to address fundamental questions about the distribution of microbes and their influence on Earth’s biogeochemical cycles. This article discusses some of the progress that scientists have made with the use of so-called “omic” techniques (metagenomics, metatranscriptomics, and metaproteomics) and the limitations and major challenges these approaches are currently facing. These ‘omic methods have been used to describe the taxonomic structure (...) of microbial communities in different environments and to discover new genes and enzymes of industrial and medical interest. However, microbial community structure varies in different spatial and temporal scales and none of the ‘omic techniques are individually able to elucidate the complex aspects of microbial communities and ecosystems. In this article we highlight the importance of a spatiotemporal sampling design, together with a multilevel ‘omic approach and a community analysis strategy (association networks and modeling) to examine and predict interacting microbial communities and their impact on the environment. (shrink)

"The Invention of Modern Science proposes a fruitful way of going beyond the apparently irreconcilable positions, that science is either "objective" or "socially constructed." Instead, suggests Isabelle Stengers, one of the most important and influential philosophers of science in Europe, we might understand the tension between scientific objectivity and belief as a necessary part of science, central to the practices invented and reinvented by scientists."--pub. desc.

This article examines Gilles Deleuze’s concept of the simulacrum, which Deleuze formulated in the context of his reading of Nietzsche’s project of “overturning Platonism.” The essential Platonic distinction, Deleuze argues, is more profound than the speculative distinction between model and copy, original and image. The deeper, practical distinction moves between two kinds of images or eidolon, for which the Platonic Idea is meant to provide a concrete criterion of selection “Copies” or icons (eikones) are well-grounded claimants to the transcendent Idea, (...) authenticated by their internal resemblance to the Idea, whereas “simulacra” (phantasmata) are like false claimants, built on a dissimilarity and implying an essential perversion or deviation from the Idea. If the goal of Platonism is the triumph of icons over simulacra, the inversion of Platonism would entail an affirmation of the simulacrum as such, which must thus be given its own concept. Deleuze consequently defines the simulacrum in terms of an internal dissimilitude or “disparateness,” which in turn implies a new conception of Ideas, no longer as self-identical qualities (the auto kath’hauto), but rather as constituting a pure concept of difference. An inverted Platonism would necessarily be based on a purely immanent and differential conception of Ideas. Starting from this new conception of the Idea, Deleuze proposes to take up the Platonic project anew, rethinking the fundamental figures of Platonism (selection, repetition, ungrounding, the question-problem complex) on a purely differential basis. In this sense, Deleuze’s inverted Platonism can at the same time be seen as a rejuvenated Platonism and even a completed Platonism. (shrink)